Brain data#

This section presents results of brain MRI data. Below are quantitative T1 values computed using the MP2RAGE and the MTsat methods. These values are averaged within the gray matter and white matter masks.

Gray matter qMRI#

Code imports#

# Python imports 
from IPython.display import clear_output
from pathlib import Path
import numpy as np
import pandas as pd

# Import custom tools
from tools.data import Data
from tools.plot import Plot

Download data#

data_type = 'brain'
release_version = 'latest'

dataset = Data(data_type)
dataset.download(release_version)
--2022-06-14 13:34:29--  https://github.com/courtois-neuromod/anat-processing/releases/download//r20210726/neuromod-anat-brain-qmri.zip
Resolving github.com (github.com)... 140.82.114.4
Connecting to github.com (github.com)|140.82.114.4|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/8209c733-4891-4342-8c30-ccd075b128f8?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220614%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220614T133429Z&X-Amz-Expires=300&X-Amz-Signature=ae1f7871012dac0e29c9d3eee5d5ac3bbdcacb05a98e81423614952c9600a988&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dneuromod-anat-brain-qmri.zip&response-content-type=application%2Foctet-stream [following]
--2022-06-14 13:34:29--  https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/8209c733-4891-4342-8c30-ccd075b128f8?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220614%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220614T133429Z&X-Amz-Expires=300&X-Amz-Signature=ae1f7871012dac0e29c9d3eee5d5ac3bbdcacb05a98e81423614952c9600a988&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dneuromod-anat-brain-qmri.zip&response-content-type=application%2Foctet-stream
Resolving objects.githubusercontent.com (objects.githubusercontent.com)... 185.199.111.133, 185.199.108.133, 185.199.109.133, ...
Connecting to objects.githubusercontent.com (objects.githubusercontent.com)|185.199.111.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 939721 (918K) [application/octet-stream]
Saving to: ‘neuromod-anat-brain-qmri.zip’

     0K .......... .......... .......... .......... ..........  5% 41.7M 0s
    50K .......... .......... .......... .......... .......... 10% 82.3M 0s
   100K .......... .......... .......... .......... .......... 16% 72.0M 0s
   150K .......... .......... .......... .......... .......... 21%  129M 0s
   200K .......... .......... .......... .......... .......... 27% 96.6M 0s
   250K .......... .......... .......... .......... .......... 32%  135M 0s
   300K .......... .......... .......... .......... .......... 38%  116M 0s
   350K .......... .......... .......... .......... .......... 43%  158M 0s
   400K .......... .......... .......... .......... .......... 49%  120M 0s
   450K .......... .......... .......... .......... .......... 54%  174M 0s
   500K .......... .......... .......... .......... .......... 59%  106M 0s
   550K .......... .......... .......... .......... .......... 65%  157M 0s
   600K .......... .......... .......... .......... .......... 70%  182M 0s
   650K .......... .......... .......... .......... .......... 76%  185M 0s
   700K .......... .......... .......... .......... .......... 81%  183M 0s
   750K .......... .......... .......... .......... .......... 87%  168M 0s
   800K .......... .......... .......... .......... .......... 92%  181M 0s
   850K .......... .......... .......... .......... .......... 98%  181M 0s
   900K .......... .......                                    100%  108M=0.008s

2022-06-14 13:34:29 (117 MB/s) - ‘neuromod-anat-brain-qmri.zip’ saved [939721/939721]
Archive:  neuromod-anat-brain-qmri.zip
  inflating: data/brain/results-neuromod-anat-brain-qmri.csv  
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  inflating: data/brain/._timeline-neuromod-anat-brain.html  

Load data plot it#

dataset.load()
fig_gm = Plot(dataset, plot_name = 'brain-1')

fig_gm.title = 'Brain gray matter qMRI microstructure'
# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_gm.display('jupyter-book', tissue = 'GM')

White matter qMRI#

fig_wm = Plot(dataset, plot_name = 'brain-2')

fig_wm.title = 'Brain white matter qMRI microstructure'
# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_wm.display('jupyter-book', tissue = 'WM')